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New Delhi metallo-beta-lactamase 1 (NDM1) mutant - H116Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 30% PEG 3350, 100 mM Sodium succinate,
Crystal Properties Matthews coefficient Solvent content 2.24 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.63 α = 87.95 b = 68.55 β = 88.82 c = 69.41 γ = 77.58
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2020-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 38.3 92.7 0.09 0.09 0.128 0.09 4.5 2 56672 20.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 88.4 0.242 0.242 0.342 0.242 3 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ZGY 1.95 30.538 56599 2785 92.574 0.225 0.2223 0.2246 0.2856 0.2874 RANDOM 26.251
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.929 1.91 -1.534 -1.628 -0.396 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 21.105 r_dihedral_angle_3_deg 16.546 r_lrange_it 7.212 r_dihedral_angle_1_deg 7.136 r_scangle_it 3.904 r_mcangle_it 3.623 r_scbond_it 2.682 r_mcbond_it 2.397 r_angle_refined_deg 1.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.926 r_dihedral_angle_4_deg 21.105 r_dihedral_angle_3_deg 16.546 r_lrange_it 7.212 r_dihedral_angle_1_deg 7.136 r_scangle_it 3.904 r_mcangle_it 3.623 r_scbond_it 2.682 r_mcbond_it 2.397 r_angle_refined_deg 1.625 r_nbtor_refined 0.309 r_symmetry_nbd_refined 0.259 r_nbd_refined 0.233 r_symmetry_xyhbond_nbd_refined 0.233 r_xyhbond_nbd_refined 0.232 r_chiral_restr 0.113 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6808 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing